Assessment by simulation of the power of a particular chip requires simulation of large sets of case and control samples which mimic the LD patterns in human populations (see Figure S1 for an example). The approach we use, implemented in a software package called HAPGEN is conceptually simple and is illustrated in Figure 1. We have previously used this approach to compare different analysis methods and has been briefly describe before [14]. In this paper we provide full details of the approach and these are given in the Methods section.
